Whilst playing around with Easystroke and trying to add a new gesture for opening a new Tomboy note,I've discovered that the tomboy --new-note command only works if tomboy itself is not running yet,otherwise it brings up the main search window again (from the minimized state),the terminal output looks like that:

(Tomboy:6452): GdkPixbuf-WARNING **: GdkPixbufLoader finalized without calling gdk_pixbuf_loader_close() - this is not allowed. You must explicitly end the data stream to the loader before dropping the last reference.

I may be wrong but that seems a buggy behavior to me,any idea on what is actually going on ?Should I file a bug on Launchpad?

There's no point in submitting this bug on Launchpad, assuming you mean Linux Mint's Launchpad. Upstream bugs you should submit upstream. Please only use Linux Mint's Launchpad to submit bugs in Linux Mint developed software (though use GitHub for Cinnamon), not for software developed in other projects. Tomboy bugs go here: https://live.gnome.org/Tomboy/Bugs. Note that Tomboy also has an IRC and a mailing list (https://live.gnome.org/Tomboy), you might want try to those before submitting a bug. And of course search their bug database for existing similar bugs first.

Ok,there was no bug reported for this,it is reproducible easily both on my LMDE installation and in a virtualbox,so I've filed one.It looks a bit weird to submit a bug to Gnome for a bug actually happening in MATE,I don't know how well they will play along with a fork of a dismissed version of their own desktop,but I'm maybe overthinking this .

Has any solution been found? As GeneC illustrated, the Tomboy menu was available in Mint 14 (MATE), integrated into the Notification Area. It functioned exactly the same as it does in the Windows version of Tomboy. In 16, there is no Tomboy icon in the Notification Area. You can add Tomboy to a panel, of course. But this always opens the Search window, making access to existing notes less convenient. Has anyone figured out a hack that restores the functionality we have lost?

Success! I added "Indicator Applet" to the panel. The tomboy pin icon appeared if Tomboy was running. The Dropbox icon also appears in this applet. Then I added tomboy to the Startup Applications list. Don't use the --panel-applet option, just "tomboy".

For me, the problem is likely due to me re-using my /home folder from Mint 14. Just today, I tried creating a new user account and found that the new user got the tomboy pin icon. The Indicator Applet is default but was not part of my old panel. In Mint 14, the Notification Area included tomboy.